How to fetch sequences from Proteinortho5 output containing all test species and no duplication in each genome

Question

[saadleeshehreen]

Hi, I want to construct a phylogenic tree on 100 Pseudomonas aeruginosa genomes. Before constructing the tree, I want to first cluster those genomes on the basis of homology and for this purpose, I am using ProteinOrtho5 software. After running the software with synteny option I want to extract protein sequences from the output those only containing all test species and no duplication in each genome. I understand I need to run grab_protein.pl on myproject.poff to do this but how can customize/filter the output before running grab_protein.pl? I followed as following proteinOrtho out put help required But grep '^4\t4' output.proteinortho didn't print anything for me. As I tested the software on 3 species, I modified it from 3 to 4. Anyone help about the filtering? Cheers

Answer 1

[h.mon]

If you run on three species, your command should be:

grep '^3\t3' output.proteinortho

Answer 2

[AlishaQ]

grep $'^3\t3' output.proteinortho

[AlishaQ]

My flavor of Linux required the $ character in front - yours might too.